<title>ndx file format</title>
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<h2>ndx file format</h2>
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<TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The GROMACS index file (usually called index.ndx) contains some
user definable sets of atoms. The file can be read by
most analysis programs, by the graphics program (<a href=ngmx.html>ngmx</a>) 
and by the preprocessor (<a href=grompp.html>grompp</a>).
Most of these programs create default index groups when no index
file is supplied, so you only need to make an index file when you need special
groups.
<p>
First the group name is written between square brackets.
The following atom numbers may be spread out over as many lines as you like.
The atom numbering starts at 1.
<p>

An example file is here:
<pre>
[ Oxygen ]
1 	4 	7 
[ Hydrogen ]
2	3	5	6
8	9
</pre>

There are two groups, and total nine atoms. The first group
<b>Oxygen</b> has 3 elements.
The second group <b>Hydrogen</b> has 6 elements.
<p>
An index file generation tool is available: <a href=make_ndx.html>make_ndx</a>.
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